Tokyo Monorail is included in the pass.
As of October 21, 2010, you can use Tokyo monorail that is operated between Haneda airport and Hamamatsucho (浜松町) by Japan Rail Pass. But you cannot exchange the actual pass because there is no Japan Railway station at Haneda airport. That means you cannot take Tokyo Monorail with no extra charge by Japan Rail Pass right after arrival at Haneda airport.
If you want to have more informations about access to Haneda, please refer this page.
Condition changed for taking Aoimori Railway
As of December 4, 2010, JAPAN RAIL PASS can be used for Aoimori Railway Line in the limited cases. If you want to take Ominato line at Noheji station, you can use Aoimori Line from Aomori or Hachinohe. But you cannot get off the train in Aoimori Railway line. And also if you use the overnight train, you have to pay the regular fare and surcharge for Aoimori Railway.
The reason why Japan Railway change the condition is starting to operate Tohoku Shinkansen between Hachinohe and Shin-Aomori. Before Tohoku Shinkansen was started to operate between Hachinohe and Shin-Aomori, this line was owned by Japan Railway. But after that, this section was transfered to the private company, Aoimori Railway. Ominato line was no longer connected with any Japan Railway lines.
Kyushu Shinkasen will be started to operate between Shin-Yatsushiro and Hakata on March 12, 2011. This section will be owned by JR Kyushu after that. I think we will not have any big changes. But Japan Railway did not announce anything about using Japan Rail Pass for Kyushu Shinkansen’ fastest train “Mizuho” and Tohoku Shinkansen’ fastest train “Hayabusa“. I will keep checking and let you know as soon as possible.
*Hayabusa except Gran Class can be used by Japan Rail Pass. But Mizuho cannot be used by Japan Rail Pass.